London Research Institute
  • London, United Kingdom
Recent publications
More than two‐thirds of cancer‐related deaths are attributable to metastases. In some tumor types metastasis can occur up to 20 years after diagnosis and successful treatment of the primary tumor, a phenomenon termed late recurrence. Metastases arise from disseminated tumor cells (DTCs) that leave the primary tumor early on in tumor development, either as single cells or clusters, adapt to new environments, and reduce or shut down their proliferation entering a state of dormancy for prolonged periods of time. Dormancy has been difficult to track clinically and study experimentally. Recent advances in technology and disease modeling have provided new insights into the molecular mechanisms orchestrating dormancy and the switch to a proliferative state. A new role for epithelial‐mesenchymal transition (EMT) in inducing plasticity and maintaining a dormant state in several cancer models has been revealed. In this review, we summarize the major findings linking EMT to dormancy control and highlight the importance of pre‐clinical models and tumor/tissue context when designing studies. Understanding of the cellular and molecular mechanisms controlling dormant DTCs is pivotal in developing new therapeutic agents that prevent distant recurrence by maintaining a dormant state.
Objectives For the present review, the following focused question was addressed: In patients with root‐analog dental implants, what is the effect of implants made of other materials than titanium (alloy) on implant survival, marginal bone loss (MBL), and technical and biological complications after at least 5 years. Materials and Methods An electronic (Medline, Embase, Web of Science) search was performed to identify observational clinical studies published from January 2000 investigating a minimum of 20 commercially available zirconia implants with a mean follow‐up of at least 60 months. Primary outcome was implant survival, secondary outcomes included peri‐implant MBL, probing depths (PDs), and technical and biological complications. Meta‐analyses were performed to evaluate implant survival, MBL, and PD. Results From 5129 titles, 580 abstracts were selected, and 111 full‐text articles were screened. Finally, 4 prospective and 2 retrospective observational clinical cohort studies were included for data extraction. Meta‐analyses estimated after 5 years of loading mean values of 97.2% (95% CI 94.7–99.1) for survival (277 implants, 221 patients), 1.1 mm (95% CI: 0.9–1.3) for MBL (229 implants, 173 patients), and 3.0 mm (95% CI 2.5–3.4) for PDs (231 implants, 175 patients). Conclusions After 5 years, commercially available zirconia implants showed reliable clinical performance based on survival rates, MBL, and PD values. However, more well‐designed prospective clinical studies and randomized clinical trials investigating titanium and zirconia implants are needed to confirm the presently evaluated promising outcomes.
Cross-national comparisons of educational achievement rely upon each participating country collecting nationally representative data. While obtaining high response rates is a key part of reaching this goal, other potentially important factors may also be at play. This paper focuses on one such issue—exclusion rates—which has received relatively little attention in the academic literature. Using data from 20 years of international large-scale assessment data, we find there to be modest variation in exclusion rates across countries and that there has been a relatively small increase in exclusion rates in some over time. We also demonstrate how exclusion rates tend to be higher in studies of primary students than in studies of secondary students. Finally, while there seems to be little relationship between exclusion rates and response rates, there is a weak negative association between the level of exclusions and test performance. We conclude by discussing how information about exclusions—and other similar issues—might be more clearly communicated to non-specialist audiences.
Brains are highly metabolically active organs, consuming 20% of a person’s energy at resting state. A decline in glucose metabolism is a common feature across a number of neurodegenerative diseases. Another common feature is the progressive accumulation of insoluble protein deposits, it’s unclear if the two are linked. Glucose metabolism in the brain is highly coupled between neurons and glia, with glucose taken up by glia and metabolised to lactate, which is then shuttled via transporters to neurons, where it is converted back to pyruvate and fed into the TCA cycle for ATP production. Monocarboxylates are also involved in signalling, and play broad ranging roles in brain homeostasis and metabolic reprogramming. However, the role of monocarboxylates in dementia has not been tested. Here, we find that increasing pyruvate import in Drosophila neurons by over-expression of the transporter bumpel , leads to a rescue of lifespan and behavioural phenotypes in fly models of both frontotemporal dementia and Alzheimer’s disease. The rescue is linked to a clearance of late stage autolysosomes, leading to degradation of toxic peptides associated with disease. We propose upregulation of pyruvate import into neurons as potentially a broad-scope therapeutic approach to increase neuronal autophagy, which could be beneficial for multiple dementias.
Background Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four of the global adult population, and ranges in severity from benign fatty liver infiltration, to hepatitis, cirrhosis, hepatocellular carcinoma, and death. NAFLD has important implications for clinical trial volunteers as an occult co-morbid condition – there is evidence that NAFLD modulates drug metabolism, with studies¹ suggesting that Grade 3–4 liver reactions are four times more common in healthy volunteers with probable NAFLD than without.This research sought to develop a non-invasive, low-cost tool, utilising supervised machine learning techniques, to predict NAFLD in a clinical trial population. Methods This is an ongoing, observational cross-sectional study with a total of 1500 clinical trial volunteers attending the unit for a single day of biomarker assessment, including bioimpedance vector analysis (visceral fat%, total body fat% and skeletal muscle%), anthropometric measurement (BMI, waist circumference), and laboratory bloods (including HBA1c, liver enzymes and WCC). A FibroScan is performed as a pragmatic gold standard ‘outcome’ for NAFLD.In this interim analysis of 570 volunteers, a logistic regression model was trained for ability to predict the outcome of the fibroscan from a data subset containing: Age, Sex, Ethnicity/Race, Height, Weight, BMI, Waist Circumference, Body Fat Percentage. The programming language R was used to build the model. The data was divided into a training set of 399 volunteers (70%) used to build the model, and 171 volunteers (30%) used to validate its predictive accuracy. Results Demographics of the included volunteers were assessed as representative of a typical early-phase population. An initial fitting of individual predictive variables into the model showed that Age, Weight, BMI, Waist Circumference and Body Fat Percentage were highly statistically significant.On fitting a full model, Age, Ethnicity/Race, and Waist Circumference were ultimately included. Weight, Height, and BMI were removed due to a high degree of collinearity, problematic to model performance. When validating the model against the volunteer test dataset, it achieved a 82.4% predictive accuracy in identifying FibroScan result. • Download figure • Open in new tab • Download powerpoint Abstract P82 Figure 1 Conclusion This preliminary model shows promising results as an early-stage clinical tool to accurately predict steatosis amongst trial volunteers.This is a group where the effective detection of concomitant, occult fatty liver disease is difficult and has significant implications for adverse drug reactions in first-in-human studies. Recruitment is expected to conclude in 2023 and, along with utilisation of the wider dataset including laboratory assessments, this is expected to improve the model’s predictive power. Reference • Takyar V, Nath A, Beri A, et al. How healthy are the “healthy volunteers”? Penetrance of NAFLD in the biomedical research volunteer pool. Hepatology 2017; 66 :825–33.
Neuronal cell loss is a defining feature of Alzheimer’s disease (AD), but the underlying mechanisms remain unclear. We xenografted human or mouse neurons into the brain of a mouse model of AD. Only human neurons displayed tangles, Gallyas silver staining, granulovacuolar neurodegeneration (GVD), phosphorylated tau blood biomarkers, and considerable neuronal cell loss. The long noncoding RNA MEG3 was strongly up-regulated in human neurons . This neuron-specific long noncoding RNA is also up-regulated in AD patients. MEG3 expression alone was sufficient to induce necroptosis in human neurons in vitro. Down-regulation of MEG3 and inhibition of necroptosis using pharmacological or genetic manipulation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, or mixed lineage kinase domain-like protein (MLKL) rescued neuronal cell loss in xenografted human neurons. This model suggests potential therapeutic approaches for AD and reveals a human-specific vulnerability to AD.
We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community.
Pulmonary arterial (PA) smooth muscle cells (PASMC) generate vascular tone in response to agonists coupled to Gq-protein receptor signaling. Such agonists stimulate oscillating calcium waves, the frequency of which drives the strength of contraction. These Ca²⁺ events are modulated by a variety of ion channels including voltage-gated calcium channels (CaV1.2), the Tmem16a or Anoctamin-1 (ANO1)-encoded calcium-activated chloride (CaCC) channel, and Ca²⁺ release from the sarcoplasmic reticulum through inositol-trisphosphate receptors (IP3R). Although these calcium events have been characterized, it is unclear how these calcium oscillations underly a sustained contraction in these muscle cells. We used smooth muscle–specific ablation of ANO1 and pharmacological tools to establish the role of ANO1, CaV1.2, and IP3R in the contractile and intracellular Ca²⁺ signaling properties of mouse PA smooth muscle expressing the Ca²⁺ biosensor GCaMP3 or GCaMP6. Pharmacological block or genetic ablation of ANO1 or inhibition of CaV1.2 or IP3R, or Ca²⁺ store depletion equally inhibited 5-HT-induced tone and intracellular Ca²⁺ waves. Coimmunoprecipitation experiments showed that an anti-ANO1 antibody was able to pull down both CaV1.2 and IP3R. Confocal and superresolution nanomicroscopy showed that ANO1 coassembles with both CaV1.2 and IP3R at or near the plasma membrane of PASMC from wild-type mice. We conclude that the stable 5-HT-induced PA contraction results from the integration of stochastic and localized Ca²⁺ events supported by a microenvironment comprising ANO1, CaV1.2, and IP3R. In this model, ANO1 and CaV1.2 would indirectly support cyclical Ca²⁺ release events from IP3R and propagation of intracellular Ca²⁺ waves.
Objectives Neurofilament light chain (NfL) has emerged as a promising biomarker for detecting and monitoring axonal injury. Until recently, NfL could only be reliably measured in cerebrospinal fluid, but digital single molecule array (Simoa) technology has enabled its precise measurement in blood samples where it is typically 50–100 times less abundant. We report development and multi-center validation of a novel fully automated digital immunoassay for NfL in serum for informing axonal injury status. Methods A 45-min immunoassay for serum NfL was developed for use on an automated digital analyzer based on Simoa technology. The analytical performance (sensitivity, precision, reproducibility, linearity, sample type) was characterized and then cross validated across 17 laboratories in 10 countries. Analytical performance for clinical NfL measurement was examined in individual patients with relapsing remitting multiple sclerosis (RRMS) after 3 months of disease modifying treatment (DMT) with fingolimod. Results The assay exhibited a lower limit of detection (LLoD) of 0.05 ng/L, a lower limit of quantification (LLoQ) of 0.8 ng/L, and between-laboratory imprecision <10 % across 17 validation sites. All tested samples had measurable NfL concentrations well above the LLoQ. In matched pre–post treatment samples, decreases in NfL were observed in 26/29 RRMS patients three months after DMT start, with significant decreases detected in a majority of patients. Conclusions The sensitivity characteristics and reproducible performance across laboratories combined with full automation make this assay suitable for clinical use for NfL assessment, monitoring in individual patients, and cross-comparisons of results across multiple sites.
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD⁺ dependent reactions together with a dedicated NADH/NAD⁺ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
BACKGROUND Glial tumours can occur in any central nervous system location, including the spinal cord. Although rare, spinal gliomas can represent a significant diagnostic challenge and are recognised as separate tumour types in the WHO classification. MATERIAL AND METHODS This study used DNA methylation profiling to characterise adult spinal glial tumours from a large neurosurgical centre, exploring relative frequencies, and the value of this technique in diagnostic workflows. A search in our laboratory information management system (2006-2021) identified 116 tumours, from patients aged 17.2-79.2 years. Diagnoses included ependymomas (all grades/subtypes) and other high- or low-grade gliomas (HGG/LGG). Extrinsic tumours (metastases, meningiomas, schwannomas) were excluded. DNA underwent methylation profiling (Illumina EPIC BeadArrays, n=116). iDat files were processed using the brain tumour classifier (MNP v12.5 R package), classifying cases against a reference cohort (n=2,800). Longitudinal (n=8) and poor QC cases (n=3) were excluded. RESULTS 83% (n=87) classified as an ependymoma (myxopapillary ependymoma (EPN_MPE, n=44), spinal ependymoma (n=43), spinal subependymoma (n=1)). We identified HGGs that were not diagnosed histologically (diffuse midline glioma, H3 K27-altered (n=2), high-grade astrocytoma with piloid features (n=1)) and 41% of cases (n=18/44) diagnosed histologically as an ependymoma, CNS WHO grade 2, classified as EPN_MPE. LGGs were less frequent (pilocytic astrocytoma (n=3), pleomorphic xanthoastrocytoma (n=1), rosette-forming glioneuronal tumour (n=1)). 9% (n=9) did not classify with existing methylation classes. Copy number analysis revealed subtype-specific changes, including prognostic alterations. CONCLUSION In conclusion, this single-centre study highlights the crucial role of DNA methylation profiling as part of diagnostic workflows for spinal glial tumours.
BACKGROUND High-grade gliomas (HGG) arise in any central nervous system location, in adults and children, with a poor prognosis. HGGs in teenagers and young adults (TYA) are understudied; this project aimed to characterise these tumours and identify potential therapeutic targets. MATERIAL AND METHODS HGG samples (n=195, FFPE/FF, 13-30 years) were collected from national/international collaborators, excluding well-characterised entities (histone/IDH-mutant). DNA methylation profiling (Illumina EPIC BeadArrays, brain tumour classifier (MNP v12.5 R package), n=195) classified cases against a reference cohort. Calibrated scores guided workflows to characterise mutational landscapes including RNA-based ArcherDx fusion panel (n=112), whole exome sequencing (n=84), and histological reviews in parallel. Well-characterised entities (n=50, including IDH-mutant tumours (n=18), PXA (n=12)) were excluded. RESULTS Of the cases scoring >0.6, 64% classified as paediatric-type subgroups (pedHGG_RTK1A/B/C (30%), pedHGG_MYCN (10%), pedHGG_A/B (7%), pedHGG_RTK2A (6%)). 29% classified as subgroups more frequently seen in adults (GBM_MES (12%), GBM_RTK1/2 (3%)). 54% classified with a score <0.6. 38% cases were assigned to novel, recently identified, poorly-characterised subgroups with distinct methylation profiles and molecular features (HGG_B, HGG_E, ANTCON, GBM_CBM). Frequency comparisons to publicly available methylation data showed GBM_MES_ATYP tumours are TYA age-specific, in contrast to adult age-specific GBM_MES_TYP. Copy number profiling identified frequent changes across the cohort, including chromosomal gains (chr1q (54%), chr2 (22%), chr7 (41%)) and losses (chr10 (40%), chr13 (64%)). Focal amplifications included PDGFRA (12%), CDK4 (7%), MYCN/ID2 (3%), MYC (2%) and EGFR (0.7%) and the most common focal deletion was CDKN2A/p16 (12%). The most frequent glioma-associated somatic variants included TP53, PDGFRA, EGFR, and NF1. BCOR alterations were enriched compared to adult and paediatric reference cohorts. 10% cases showed a hypermutator phenotype, enriched in HGG_E. CDK4 amplifications were recurrent in GBM_RTK1 and GBM_CBM. Histology showed variable cytological and architectural features within novel subgroups. CONCLUSION TYA HGG comprise novel subgroups with distinct methylation profiles and molecular characteristics, representing opportunities to refine future treatment.
Background Physical activity in childhood is thought to influences health and development. Previous studies have found that boys are typically more active than girls, yet the focus has largely been on differences in average levels or proportions above a threshold rather than the full distribution of activity across all intensities. We thus examined differences in the distribution of physical activity between girls and boys in a multi-national sample of children. Methods We used the harmonised International Children Accelerometry Database (ICAD), including waist-worn accelerometry data from 15,461 individuals (Boys: 48.3%) from 9 countries. Employing Generalised Additive Models of Location, Shape, and Scale (GAMLSS) we investigated gender differences in the distribution of individuals, including comparisons of variability (SD) and average physical activity levels (mean and median) and skewness. We conducted this analysis for each activity intensity (Sedentary, Light, and Moderate-to-Vigorous (MVPA)) and a summary measure (counts per minute (CPM)). Results Sizable gender differences in the distribution of activity were found for moderate to vigorous activity and counts per minute, with boys having higher average levels (38% higher mean volumes of MVPA, 20% higher CPM), yet substantially more between-person variability (30% higher standard deviation (SD) for MVPA, 17% higher SD for CPM); boys’ distributions were less positively skewed than girls. Conversely, there was little to no difference between girls and boys in the distribution of sedentary or light-intensity activity. Conclusions Inequality in activity between girls and boys was driven by MVPA. The higher mean volumes of MVPA in boys occurred alongside greater variability. This suggests a need to consider the underlying distribution of activity in future research; for example, interventions which target gender inequality in MVPA may inadvertently lead to increased inequality within girls.
Purpose: No consensus exists on the management of men with nonseminoma and viable nonteratomatous germ cell tumor in the postchemotherapy retroperitoneal lymph node dissection (pcRPLND) specimen after first-line chemotherapy. We analyzed surveillance versus different adjuvant chemotherapy regimens and the influence of time to pcRPLND on oncologic outcomes. Methods: Data on 117 men treated with cisplatin-based first-line chemotherapy between 1990 and 2018 were collected from 13 institutions. All patients had viable nonteratomatous germ cell tumor in the pcRPLND specimen. Surgery was performed after a median of 57 days, followed by either surveillance (n = 64) or adjuvant chemotherapy (n = 53). Primary end points were progression-free survival (PFS), cancer-specific survival (CSS), and overall survival (OS). Results: After controlling for International Germ Cell Cancer Cooperative Group risk group and percent of viable malignant cells found at RPLND, no difference was observed between men managed with surveillance or adjuvant chemotherapy regarding PFS (hazard ratio [HR], 0.72 [95% CI, 0.32 to 1.6]; P = .4), CSS (HR, 0.69; 95% CI, 0.20 to 2.39; P = .6), and OS (HR, 0.78 [95% CI, 0.25 to 2.44]; P = .7). No statistically significant differences for PFS, CSS, or OS were observed on the basis of chemotherapy regimen or in men treated with pcRPLND ≤57 versus >57 days after first-line chemotherapy. Residual disease with <10% versus ≥10% viable cancer cells were associated with a longer PFS (HR, 3.22 [95% CI, 1.29 to 8]; P = .012). Relapse in the retroperitoneum was observed in 34 (29%) men. Conclusion: Men with a complete resection at pcRPLND and <10% viable cells have favorable outcomes without further treatment. Complete retroperitoneal resection seems more important than early pcRPLND.
The locus coeruleus (LC) is an important noradrenergic nucleus that has recently attracted a lot of attention because of its emerging role in cognitive and psychiatric disorders. Although previous histological studies have shown that the LC has heterogeneous connections and cellular features, no studies have yet assessed its functional topography in vivo, how this heterogeneity changes over aging, and whether it is associated with cognition and mood. Here, we employ a gradient-based approach to characterize the functional heterogeneity in the organization of the LC over aging using 3T resting-state fMRI in a population-based cohort aged from 18 to 88 years of age (Cambridge Centre for Ageing and Neuroscience cohort, n=618). We show that the LC exhibits a rostro-caudal functional gradient along its longitudinal axis, which was replicated in an independent dataset (Human Connectome Project [HCP] 7T dataset, n=184). Although the main rostro-caudal direction of this gradient was consistent across age groups, its spatial features varied with increasing age, emotional memory, and emotion regulation. More specifically, a loss of rostral-like connectivity, more clustered functional topography, and greater asymmetry between right and left LC gradients was associated with higher age and worse behavioral performance. Furthermore, participants with higher-than-normal Hospital Anxiety and Depression Scale (HADS) ratings exhibited alterations in the gradient as well, which manifested in greater asymmetry. These results provide an in vivo account of how the functional topography of the LC changes over aging, and imply that spatial features of this organization are relevant markers of LC-related behavioral measures and psychopathology.
Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson's disease (PD) and Alzheimer's disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.
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36 members
Gordon Stamp
  • Experimental Histopathology
Tammy MK Cheng
  • Biomolecular Modelling Lab
Gary Hong Chun Chung
  • Cell Biophysics Lab
Nil Ege
  • Tumour Cell Biology
London, United Kingdom